Merge pull request #120 from inbo/bugfix

Version 0.3.6

.Rbuildignore

@@ -18,5 +18,6 @@
 ^docker-compose.test.yml$
 ^docs$
 ^man-roxygen$
+^organisation.yml$
 ^pkgdown$
 ^test_docker.sh$

.github/CODE_OF_CONDUCT.md

@@ -8,7 +8,7 @@ We are committed to making participation in this project a harassment-free exper
 everyone, regardless of level of experience, gender, gender identity and expression,
 sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or religion.
 
-Examples of unacceptable behavior by participants include the use of sexual language or
+Examples of unacceptable behaviour by participants include the use of sexual language or
 imagery, derogatory comments or personal attacks, trolling, public or private harassment,
 insults, or other unprofessional conduct.
 
@@ -17,7 +17,7 @@ commits, code, wiki edits, issues, and other contributions that are not aligned
 Code of Conduct. Project maintainers who do not follow the Code of Conduct may be removed 
 from the project team.
 
-Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by 
+Instances of abusive, harassing, or otherwise unacceptable behaviour may be reported by 
 opening an issue or contacting one or more of the project maintainers.
 
 This Code of Conduct is adapted from the Contributor Covenant 

.github/CONTRIBUTING.md

@@ -3,22 +3,22 @@
 ### Fixing typos
 
 Small typos or grammatical errors in documentation may be edited directly using the GitHub web interface, so long as the changes are made in the _source_ file.
-E.g. edit a roxygen comment in a `.R` file below `R/`, not in an `.Rd` file below `man/`.
+E.g. edit a `roxygen2` comment in a `.R` file below `R/`, not in an `.Rd` file below `man/`.
 
 ### Prerequisites
 
 Before you make a substantial pull request, you should always file an issue and make sure someone from the team agrees that it’s a problem. 
-If you’ve found a bug, create an associated issue and illustrate the bug with a minimal [reprex](https://www.tidyverse.org/help/#reprex).
+If you’ve found a bug, create an associated issue and illustrate the bug with a minimal [reproducible example](https://www.tidyverse.org/help/#reprex).
 
 ### Pull request process
 
 *  We recommend that you create a Git branch for each pull request (PR).  
 *  Look at the GitHub Actions build status before and after making changes.
 The `README` should contain badges for any continuous integration services used by the package.  
-*  We require the tidyverse [style guide](http://style.tidyverse.org).
-You can use the [styler](https://CRAN.R-project.org/package=styler) package to apply these styles, but please don't restyle code that has nothing to do with your PR.  
-*  We use [roxygen2](https://cran.r-project.org/package=roxygen2).  
-*  We use [testthat](https://cran.r-project.org/package=testthat). 
+*  We require the `tidyverse` [style guide](http://style.tidyverse.org).
+You can use the [`styler`](https://CRAN.R-project.org/package=styler) package to apply these styles, but please don't restyle code that has nothing to do with your PR.  
+*  We use [`roxygen2`](https://cran.r-project.org/package=roxygen2).  
+*  We use [`testthat`](https://cran.r-project.org/package=testthat). 
 Contributions with test cases included are easier to accept.  
 *  For user-facing changes, add a bullet to the top of `NEWS.md` below the current development version header describing the changes made followed by your GitHub username, and links to relevant issue(s)/PR(s).
 
@@ -36,4 +36,4 @@ email is totally warranted if it's a sensitive problem of any kind.
 
 ### Thanks for contributing!
 
-This contributing guide is adapted from the tidyverse contributing guide available at https://raw.githubusercontent.com/r-lib/usethis/master/inst/templates/tidy-contributing.md 
+This contributing guide is adapted from the `tidyverse` contributing guide available at https://raw.githubusercontent.com/r-lib/usethis/master/inst/templates/tidy-contributing.md 

.github/workflows/check_on_branch.yml

@@ -4,7 +4,7 @@ on:
       - main
       - ghpages
 
-name: "check package"
+name: "check package with checklist"
 
 jobs:
   check-package:
@@ -17,4 +17,4 @@ jobs:
     permissions:
       contents: read
     steps:
-      - uses: inbo/actions/check_pkg@main
+      - uses: inbo/actions/check_pkg@checklist-0.3.6

.github/workflows/check_on_different_r_os.yml

@@ -2,13 +2,9 @@ on:
   push:
     branches:
       - main
-      - master
   pull_request:
     branches:
       - main
-      - master
-  schedule:
-    - cron: '6 0 * * 1'
 
 name: R-CMD-check-OS
 
@@ -44,6 +40,7 @@ jobs:
 
       - uses: r-lib/actions/setup-pandoc@v2
 
+
       - name: linux dependencies
         if: runner.os == 'linux'
         run: |

.github/workflows/check_on_main.yml

@@ -2,14 +2,11 @@ on:
   push:
     branches:
       - main
-      - master
-  schedule:
-    - cron: '6 0 15 * *'
-
-name: "check package on main"
 permissions:
   contents: write
 
+name: "check package on main with checklist"
+
 jobs:
   check-package:
     runs-on: ubuntu-latest
@@ -19,4 +16,4 @@ jobs:
       GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       ZENODO_SANDBOX: ${{ secrets.ZENODO_SANDBOX }}
     steps:
-      - uses: inbo/actions/check_pkg@main
+      - uses: inbo/actions/check_pkg@checklist-0.3.6

.github/workflows/release.yml

@@ -10,28 +10,21 @@ on:
       - completed
 
 jobs:
-  prepare:
+  publish:
     runs-on: ubuntu-latest
-    outputs:
-      tag: ${{ steps.gettag.outputs.tag }}
-      body: ${{ steps.gettag.outputs.body }}
+    permissions:
+      contents: write
     steps:
       - uses: actions/checkout@v3
       - name: Get tag
         run: |
           git fetch --tags --force
           TAG=$(git tag --contains $(git rev-parse HEAD))
-          echo "tag=$TAG" >> "$GITHUB_OUTPUT"
-          echo "body=$TAG_BODY" >> "$GITHUB_OUTPUT"
-        id: gettag
-  publish:
-    runs-on: ubuntu-latest
-    permissions:
-      contents: write
-    needs: prepare
-    steps:
+          TAG_BODY=$(git tag --contains $(git rev-parse HEAD) --format='%(contents)')
+          echo "tag=$TAG" >> $GITHUB_ENV
+          echo "$TAG_BODY" > body.md
       - uses: ncipollo/release-action@v1
         with:
-          name: Release ${{needs.prepare.outputs.tag}}
-          tag: ${{needs.prepare.outputs.tag}}
-          body: ${{needs.prepare.outputs.body}}
+          name: Release ${{ env.tag }}
+          tag: ${{ env.tag }}
+          bodyFile: body.md

.gitignore

@@ -1,12 +1,28 @@
+
+# OAuth tokens
 # Rstudio
-.Rproj.user
-.Rhistory
+# pkgdown
+*.dbf
+*.doc*
+*.gddoc
+*.gdsheet
+*.gpkg
+*.html
+*.mdb
+*.shp*
+*.shx
+*.xls*
+*_files
+.DS_Store
 .RData
+.Renviron
+.Rhistory
+.Rproj.user
 .Ruserdata
-
-# OAuth tokens
 .httr-oauth
-
-# pkgdown
+docs
 docs/*
 inst/doc
+libs
+output
+renv/library

.zenodo.json

@@ -1,9 +1,9 @@
 {
   "title": "checklist: A Thorough and Strict Set of Checks for R Packages and Source Code",
-  "version": "0.3.5",
+  "version": "0.3.6",
   "license": "GPL-3.0",
   "upload_type": "software",
-  "description": "<p>An opinionated set of rules for R packages and R source code\nprojects.<\/p>",
+  "description": "<p>An opinionated set of rules for R packages and R source code projects.<\/p>",
   "keywords": [
     "quality control",
     "documentation",
@@ -16,23 +16,23 @@
       "name": "Onkelinx, Thierry",
       "affiliation": "Research Institute for Nature and Forest (INBO)",
       "orcid": "0000-0001-8804-4216",
-      "type": "ContactPerson"
+      "type": "contactperson"
     },
     {
       "name": "Lommelen, Els",
       "affiliation": "Research Institute for Nature and Forest (INBO)",
       "orcid": "0000-0002-3481-5684",
-      "type": "ProjectMember"
+      "type": "projectmember"
     },
     {
       "name": "Van Calster, Hans",
       "affiliation": "Research Institute for Nature and Forest (INBO)",
       "orcid": "0000-0001-8595-8426",
-      "type": "ProjectMember"
+      "type": "projectmember"
     },
     {
       "name": "Research Institute for Nature and Forest (INBO)",
-      "type": "RightsHolder"
+      "type": "rightsholder"
     }
   ],
   "creators": [

CITATION.cff

@@ -1,6 +1,6 @@
 cff-version: 1.2.0
 message: If you use this software, please cite it using these metadata.
-title: 'checklist: A Thorough and Strict Set of Checks for R Packages and Source Code'
+title: "checklist: A Thorough and Strict Set of Checks for R Packages and Source Code"
 authors:
 - given-names: Thierry
   family-names: Onkelinx
@@ -19,10 +19,10 @@ doi: 10.5281/zenodo.4028303
 license: GPL-3.0
 repository-code: https://github.com/inbo/checklist/
 type: software
-abstract: An opinionated set of rules for R packages and R source code projects.
+abstract: "An opinionated set of rules for R packages and R source code projects."
 identifiers:
 - type: doi
   value: 10.5281/zenodo.4028303
 - type: url
   value: https://inbo.github.io/checklist/
-version: 0.3.5
+version: 0.3.6

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: checklist
 Title: A Thorough and Strict Set of Checks for R Packages and Source Code
-Version: 0.3.5
+Version: 0.3.6
 Authors@R: c(
     person("Thierry", "Onkelinx", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-8804-4216", affiliation = "Research Institute for Nature and Forest (INBO)")),
@@ -21,6 +21,7 @@ Depends:
     R (>= 4.1.0)
 Imports:
     assertthat,
+    cli,
     codemetar,
     desc,
     devtools (> 2.4.0),
@@ -50,14 +51,13 @@ Suggests:
     showtext,
     sysfonts,
     testthat,
-    zen4R (>= 0.9)
+    zen4R (>= 0.10)
 VignetteBuilder: 
     knitr
-Additional_repositories: https://inbo.r-universe.dev
 Config/checklist/communities: inbo
 Config/checklist/keywords: quality control; documentation; publication
 Encoding: UTF-8
 Language: en-GB
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 SystemRequirements: Pandoc (>= 1.17.2)